Mods not deploying and updates only disabling original version

[maddlarkin]

Hey, anyone else having these issues, I download a mod, enable it, it deploys but when I go and check the plugins on the load order all I see '??????' instead of a number in the load order and if I load the game mods not present, if I flick the ordering to manual then return it to automatic it will deploy and get a number then appear properly in the load order. Have I cocked up a setting some where while fighting the cat round the keyboard?

 

Also I've noticed since last update when updating to a new version of an existing mod (something Fallout 4 updates breaking F4SE makes me do with horrendous frequency) it disables the original version then enables the new on leaving them in parallel causing it not to enable properly. Only work around I've found is to uninstall the mod completely then enable the new one from fresh, of course here I hit the deployment issue again (this one honestly could be a setting thing from aforementioned cat fighting issue)